Rename everything to brainmapper and explicitly support old cellfinde…

…r directories

brainglobe_napari_io/workflows/wholebrain_cell_reader_dir.py → brainglobe_napari_io/brainmapper/brainmapper_reader_dir.py

@@ -1,7 +1,7 @@
 import json
 import os
 from pathlib import Path
-from typing import Callable, List, Optional, Tuple, Union
+from typing import Callable, Dict, List, Optional, Tuple, Union
 
 import bg_space as bgs
 from napari.types import LayerDataTuple
@@ -14,22 +14,25 @@
 PathOrPaths = Union[List[os.PathLike], os.PathLike]
 
 
-def is_wholebrain_cell_dir(path: os.PathLike) -> bool:
+def is_brainmapper_dir(path: os.PathLike) -> bool:
     """
-    Determines whether a path is to a BrainGlobe workflows whole brain
+    Determines whether a path is to a BrainGlobe brainmapper whole brain
     cell detection (previously cellfinder) output directory.
     """
     path = os.path.abspath(path)
     if os.path.isdir(path):
         filelist = os.listdir(path)
     else:
         return False
-    if "cellfinder.json" in filelist:
+    if "brainmapper.json" in filelist:
+        return True
+    # for backwards compatibility
+    elif "cellfinder.json" in filelist:
         return True
     return False
 
 
-def wholebrain_cell_read_dir(path: PathOrPaths) -> Optional[Callable]:
+def brainmapper_read_dir(path: PathOrPaths) -> Optional[Callable]:
     """A basic implementation of the napari_get_reader hook specification.
 
     Parameters
@@ -43,12 +46,23 @@ def wholebrain_cell_read_dir(path: PathOrPaths) -> Optional[Callable]:
         If the path is a recognized format, return a function that accepts the
         same path or list of paths, and returns a list of layer data tuples.
     """
-    if isinstance(path, str) and is_wholebrain_cell_dir(path):
+    if isinstance(path, str) and is_brainmapper_dir(path):
         return reader_function
     else:
         return None
 
 
+def get_metadata(directory: Path) -> Dict:
+    try:
+        with open(directory / "brainmapper.json") as json_file:
+            metadata = json.load(json_file)
+    # for backwards compatibility
+    except FileNotFoundError:
+        with open(directory / "cellfinder.json") as json_file:
+            metadata = json.load(json_file)
+    return metadata
+
+
 def reader_function(
     path: os.PathLike,
     point_size: int = 15,
@@ -78,10 +92,9 @@ def reader_function(
         layer_type=="image" if not provided
     """
 
-    print("Loading whole brain cell detection directory")
+    print("Loading brainmapper directory")
     path = Path(os.path.abspath(path))
-    with open(path / "cellfinder.json") as json_file:
-        metadata = json.load(json_file)
+    metadata = get_metadata(path)
 
     layers: List[LayerDataTuple] = []
 

brainglobe_napari_io/napari.yaml

@@ -10,9 +10,9 @@ contributions:
     title: Brainreg Read Directory Atlas Space
     python_name: brainglobe_napari_io.brainreg.reader_dir_atlas_space:brainreg_read_dir_atlas_space
 
-  - id: brainglobe-napari-io.workflows_wholebrain_cell_read_dir
-    title: Workflows Whole Brain Cell Detection Read Directory
-    python_name: brainglobe_napari_io.workflows.wholebrain_cell_reader_dir:wholebrain_cell_read_dir
+  - id: brainglobe-napari-io.brainmapper_read_dir
+    title: Brainmapper Read Directory
+    python_name: brainglobe_napari_io.brainmapper.brainmapper_reader_dir:brainmapper_read_dir
 
   - id: brainglobe-napari-io.cellfinder_read_xml
     title: Cellfinder Read XML
@@ -34,7 +34,7 @@ contributions:
       - '*.tiff'
     accepts_directories: true
 
-  - command: brainglobe-napari-io.workflows_wholebrain_cell_read_dir
+  - command: brainglobe-napari-io.brainmapper_read_dir
     filename_patterns:
     - '*.tif'
     accepts_directories: true

tests/data/brainmapper_output/brainmapper.json

@@ -0,0 +1 @@
+{"signal_planes_paths": ["2"], "background_planes_path": ["4"], "output_dir": "output", "signal_ch_ids": null, "background_ch_id": null, "registration_config": "cellfinder.conf.custom", "voxel_sizes": ["5", "2.31", "2.31"], "network_voxel_sizes": [5, 1, 1], "no_detection": false, "no_classification": false, "no_register": false, "no_analyse": false, "no_figures": false, "start_plane": 0, "end_plane": -1, "save_planes": false, "outlier_keep": false, "artifact_keep": false, "max_cluster_size": 100000, "soma_diameter": 16, "ball_xy_size": 6, "ball_z_size": 15, "ball_overlap_fraction": 0.6, "log_sigma_size": 0.2, "n_sds_above_mean_thresh": 10, "soma_spread_factor": 1.4, "trained_model": "model.h5", "model_weights": null, "network_depth": "50", "batch_size": 64, "cube_width": 50, "cube_height": 50, "cube_depth": 20, "save_empty_cubes": false, "n_free_cpus": 8, "max_ram": null, "save_csv": false, "debug": false, "sort_input_file": false, "no_models": false, "model": "resnet50_tv", "heatmap_smooth": 100, "mask_figures": true, "install_path": ".cellfinder", "download_path": "tmp", "no_amend_config": false, "atlas": "allen_mouse_100um", "orientation": "prs", "backend": "niftyreg", "affine_n_steps": 6, "affine_use_n_steps": 5, "freeform_n_steps": 6, "freeform_use_n_steps": 4, "bending_energy_weight": 0.95, "grid_spacing": -10, "smoothing_sigma_reference": -1.0, "smoothing_sigma_floating": -1.0, "histogram_n_bins_floating": 128, "histogram_n_bins_reference": 128, "paths": {"output_dir": "output_dir", "registration_output_folder": "output_dir/brainreg_output", "metadata_path": "output/brainmapper.json", "registration_metadata_path": "output_dir/brainreg_output/brainreg.json"}}